SMTL ID : 3uxk.1 (1 other biounit)

P. putida mandelate racemase co-crystallized with the intermediate analogue benzohydroxamate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-octamer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 7 residues within 4Å: Chain A: K.188, K.190, D.219, N.221, E.245, E.271 Ligands: BHO.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.219, A:E.245, A:E.271, H2O.8 MG.3: 7 residues within 4Å: Chain B: K.188, K.190, D.219, N.221, E.245, E.271 Ligands: BHO.4 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.219, B:E.245, B:E.271, H2O.14 MG.5: 7 residues within 4Å: Chain C: K.188, K.190, D.219, N.221, E.245, E.271 Ligands: BHO.6 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.219, C:E.245, C:E.271, H2O.22 MG.7: 7 residues within 4Å: Chain D: K.188, K.190, D.219, N.221, E.245, E.271 Ligands: BHO.8 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.219, D:E.245, D:E.271, H2O.28 MG.9: 7 residues within 4Å: Chain E: K.188, K.190, D.219, N.221, E.245, E.271 Ligands: BHO.10 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.219, E:E.245, E:E.271, H2O.36 MG.11: 7 residues within 4Å: Chain F: K.188, K.190, D.219, N.221, E.245, E.271 Ligands: BHO.12 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.219, F:E.245, F:E.271, H2O.42 MG.13: 7 residues within 4Å: Chain G: K.188, K.190, D.219, N.221, E.245, E.271 Ligands: BHO.14 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.219, G:E.245, G:E.271, H2O.50 MG.15: 7 residues within 4Å: Chain H: K.188, K.190, D.219, N.221, E.245, E.271 Ligands: BHO.16 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:D.219, H:E.245, H:E.271, H2O.56

8 x BHO: BENZHYDROXAMIC ACID(Non-covalent)

BHO.2: 12 residues within 4Å: Chain A: V.46, F.76, K.188, K.190, D.219, N.221, E.245, E.271, H.321, E.341, L.343 Ligands: MG.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.46, A:F.76, A:L.343 Hydrogen bonds: A:K.188, A:K.190, A:D.219, A:D.219, A:N.221, A:E.341 BHO.4: 10 residues within 4Å: Chain B: V.46, K.188, K.190, D.219, N.221, E.245, E.271, H.321, E.341 Ligands: MG.3 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.46 Hydrogen bonds: B:K.188, B:K.190, B:D.219, B:N.221, B:E.341 BHO.6: 12 residues within 4Å: Chain C: V.46, F.76, K.188, K.190, D.219, N.221, E.245, E.271, H.321, E.341, L.343 Ligands: MG.5 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:V.46, C:F.76, C:L.343 Hydrogen bonds: C:K.188, C:K.190, C:D.219, C:D.219, C:N.221, C:E.341 BHO.8: 10 residues within 4Å: Chain D: V.46, K.188, K.190, D.219, N.221, E.245, E.271, H.321, E.341 Ligands: MG.7 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:V.46 Hydrogen bonds: D:K.188, D:K.190, D:D.219, D:N.221, D:E.341 BHO.10: 12 residues within 4Å: Chain E: V.46, F.76, K.188, K.190, D.219, N.221, E.245, E.271, H.321, E.341, L.343 Ligands: MG.9 9 PLIP interactions: 9 interactions with chain E Hydrophobic interactions: E:V.46, E:F.76, E:L.343 Hydrogen bonds: E:K.188, E:K.190, E:D.219, E:D.219, E:N.221, E:E.341 BHO.12: 10 residues within 4Å: Chain F: V.46, K.188, K.190, D.219, N.221, E.245, E.271, H.321, E.341 Ligands: MG.11 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:V.46 Hydrogen bonds: F:K.188, F:K.190, F:D.219, F:N.221, F:E.341 BHO.14: 12 residues within 4Å: Chain G: V.46, F.76, K.188, K.190, D.219, N.221, E.245, E.271, H.321, E.341, L.343 Ligands: MG.13 9 PLIP interactions: 9 interactions with chain G Hydrophobic interactions: G:V.46, G:F.76, G:L.343 Hydrogen bonds: G:K.188, G:K.190, G:D.219, G:D.219, G:N.221, G:E.341 BHO.16: 10 residues within 4Å: Chain H: V.46, K.188, K.190, D.219, N.221, E.245, E.271, H.321, E.341 Ligands: MG.15 7 PLIP interactions: 7 interactions with chain H Hydrophobic interactions: H:V.46 Hydrogen bonds: H:K.188, H:K.190, H:N.221, H:E.245, H:E.341 Water bridges: H:E.245

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lietzan, A.D. et al., Structure of mandelate racemase with bound intermediate analogues benzohydroxamate and cupferron. Biochemistry (2012)

Release Date

2012-02-08

Peptides

Mandelate racemase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
A

D
C

E
A

F
C

G
A

H
C

Mandelate racemase

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